I posted this by mistake in the 05-12 section so I wanted to post it in the correct 99-04 section for you guys, sorry for the length but I wanted to explain my whole process... Read the red text if you just want to see what the problem was and how I fixed it.I have been driving the car for a week now since I fixed it and it runs like a dream!

I have a 2000 GT, 5 speed with 223k miles on it(yeah it's a lot but I take real good care of it) with some minor engine and exhaust upgrades and a brenspeed tune but nothing crazy. For months upon months now I was having the well known "low rpm hesitation/misfire that would smooth out above about 2000 rpm" problem. The only code it ever threw was a P0171 lean code but I knew that was due to an exhaust leak. Looking around in the forums it seems that these symptoms are relatively common with the 99-04's and no one(at least that I could find) ever really found the reason for these symptoms. Hopefully what I've found out will help some of you out there with the same issues I was having.

Having that many miles, things are bound to be worn out so I started replacing stuff because it really needed it anyways, here is the order of stuff I replaced in my quest to fix the dreaded hesitation/misfire:

Cleaned and re-oiled air filter
COP's - ran better first few mins but hesitation returned
IAC - fixed the stalling out at idle problem, but not the hesitation
Verified TPS was good - was good
Cleaned MAF - didn't do a damn thing
PCV - it just needed a new one but then I realized I had vacuum issues
Vacuum lines - replaced bad rubber lines but still had hesitation
Alternator - diode had gone out on ORIGINAL one, lol
New MAC Prochamber - Original one was rusting through
Fuel filter - time for a new one anyway
New injectors - yeah, they were original too, ran better but still no fix
Cleaned Throttle Body - was filthy but hesitation was still there

All throughout the above process I was searching all the forums to see what I could/should try next
Part of me was saying that maybe I will just have to accept this issue because there are so many miles on the engine and perhaps it was just starting to crap out from wear...

Next possible steps were to check the cam position sensor, the crank sensor, blah blah blah...

Last night I was so over the whole thing I just went back to square 1 and re-thought the problem... I'm an electrical engineer and I just cannot let seemingly simple problems like this go. The best way to describe the symptom is it's almost identical to having just washed the engine and having water in the spark plug wells causing the engine to "skip". That has happened to me in the past but it always goes away after some driving to evapoate the water. So, I took out the COP's 1 by 1 and verified that the plug wells were dry and that the plugs were not loose. Everything was dry as a bone and all plugs were tight. Reassembled everything and started the engine only to have a constant miss where before it was only an intermittent miss at idle!!!! So I made things worse

I remained calm and knew that the only things I touched were the COP's and now I had a constant miss which actually gave me a good opportunity. What I did was unplug each COP, 1 at a time to see if the idle was affected. When I got to the one where there was no change in the idle - that was the COP/cyl causing the miss. Sure enough, 3rd one I tried, cyl.7, had no change when I unplugged the COP. Now I knew exactly where to focus on. I pulled out that COP, plugged in an old plug laying around and started the engine to verify it was producing spark, and it was so WTF?!

Just for giggles I also tested one of my original COP's with the extra plug and it worked too, so I reinstalled the old COP on cyl. 7 and started the engine. It ran fine so now I was really like WTF?!

I turned my attention to the harness connector that plugs onto the COP and the tab that is supposed to keep it from backing off was not there(never has been there best I can tell) so although the connector was "connected", there was nothing keeping the connector from backing off. I pushed on the connector and got it to fully seat but as soon as I took my finger off, it would slide back a little from the dielectric grease I had on the connectors. At that moment it was like angels descended out of heaven singing the Hallelujah Chorus and I finally figured it out! Even though the connector was seemingly "connected" it would slide back just enough to break the contact to the COP pins. This explains why the car ran fine just after installing new plugs, the connector was seated enough right after install but backed off from vibration.

What I did to fix this was take a 12" zip tie(I think it was 12") and feed it between the 2 wires on the back of the connector that plugs onto the COP and loop it around the "ear" on the COP that sticks out and has the screw hole for mounting to the intake. They are not going anywhere now.
For whatever reason, only like 2 or 3 of my COP connectors had the tab intact that would keep them from backing off so I put a zip tie on each of them.

Drove it to work this morning and it was like driving a new car! After living with that annoying misfire/hesitation for so long I had forgotten just how fun this car was to drive!

Hopefully this will help some other people out there and save them some money, all you need is a few zip ties. Not to say that this is the end all be all fix for everyone's hesitation issue, but it sure was for mine and it will give you something to rule out if nothing else. Feel free to email me and I will be happy to send pics of what I did.

Thanks to all of you who post to these forums, you have been an invaluable resource for me and are a great resource for all of us!

great writeup, congrats on the discovery, and on finding an excuse to replace all those other items! had a similar problem with my f150 recently, started by replacing the plugs/wires, yet still had the miss. turns out when i was realigning my coil wires (yes, its non-COP) i must've tugged too hard on one of the rear-most cylinders and pulled the boot off. of course that was the last possible problem i could have thought of, so i started cleaning or replacing all the little knick knacks as well. major face palm on that one!

I know this thread is old but it should be the first thread to appear when doing a google search for 4.6 misfire, stutter, etc. Just like everyone else it seems I replaced way to much unneeded parts finally buying 8 MSD COP's thinking that will fix the problem for sure since it seemed to be obviously electrical. (small to moderate studder/hesitation under acceleration after 4th gear. Once it down shifted under moderate accel. or WOT wouldn't miss a beat) but after changing everything = roughly 800$ including MSD's the problem persisted.

Removing the COP's became a weekend affair looking for the problem, and similar to 110 leaded's situation mine would seemingly be fixed for the very beginning of the first trip after but half way through every time the stutter returned.

So, after finally saying to myself I am not wasting any more time or $ on this and just lived with it, driving to and from work either coasting or WOT ( pretty funny at first in a TC), but became very annoying when trying to have a relaxing drive with the family to church.

After 4-6 months of living with it I stumbled onto a mustang forum (here) and found the solution in 10 cent zip ties THX TO 110 leaded!!!

Did the zip ties in under 5 minutes right after reading and everything is great, I will probably replace the plug connectors soon but there is no rush at this point.

I did every single step by the book, buying the expensive/quality parts, using di-electric grease on everything (even those d@mn plug connectors!) fuel cleaner, replaced the auto-tranny fluid x2 with filters, bought 3-4 motocraft COP'st to get a full set of MSD's, checked injectors, x2 or 3 sets of different brands of the 6-8$ plugs each, air filters, clean mass air flow sensor.

After all that which I am sure I'm not the only one, to not have this thing running like a top was very frustrating, especially since this isn't a project car, it's my daily driver.

On the other hand, I have to say it gave me a chance to work under the hood I love my 4.6, easy to work on (even those darn plugs near the fire wall) and I am chevy guy at heart but I love this thing more than ever now!

Thx for reading guys/gals and let me know if ya'll want a update after a few thousand miles later.

I have this same problem on mine except i have coil packs(lol). does anyone have any suggestions as to want i should do? Im considering MSD coil packs and wires anyway but until i get to that point, i would like to fix this annoying problem. Its also embarrasing when taking the girlfriend out and having the car hesitate.

i just got my dream stang a couple months ago and i have been tuning it up ever since i got it! i love working on my stang.. having 205k miles on my 03 gt isn't too bad but it just means a lot of TLC to get her running right again. started out with the basics...

oil change + oil filter performance of course
all spark plugs Bosch+4 platinum quad spark = awesome
changed 4 cops 1,2,7,8
took fuel rail off and cleaned the injectors
broke the heater line on the firewall so i replaced that
already had a coldair kn&n so recharged the filter = less i have to buy
clean all accessible sensors maf, mas air, throttle body, everything else
water pump broke 3 weeks ago had to replace that = scary screeching sound
replace both indle pulleys = just felt like replacing them
just did the big job of changing the clutch = it will be easier next time
replaced the breaks all the way around pads and rotors
found that the elbow before the pvc was clogged = replaced hose
nipply new tires

thats all i have done to my baby so far... i had this dreaded misfire...
sluggish starting, shifting hard, crusing between 1100 and 1800 rpms seemed anoying and depressing. best discribing of the mis was it felt like someone in a big truck was attached to my bumper tapping his breaks and hitting the gas at the same time every 1-2 secs.... almost like having a bad cold coughing all the time...

anyways i love talking about my stang till im blue in the face...

this ZIP TIE!?!?! trick is awesome!!! it worked immediately!! amazing difference in starting, shifting, and cruzing... there is no misfire anymore...
just drove it today back and forth to work... awesome awesome awesome...

i only have one problem to try and fix... my brand new breaks squeak and rattle squeak ... regular brand new rotors padded with gold ceramics on all 4 rotors... i have always changed my own breaks and i have never had a problem... i have done probably 20 break jobs.. so not a newbe.. when i changed the breaks in the front owners before me had damaged the face of the piston where the pad contacts... whoever did the break job before me didnt realize that the pads with rivets exposed go to the outside, not the inside. so i cleaned up the face of the piston and put it all together. the rear break were stuck closed... standard c-clamp wouldnt compress the piston. i had to remove the calipers and beat the piston down till it got past the pinch point.. after i got the calipers free again the rear calipers moved easily again.. the breaks were neglected.

all in all its been fun working on her... i just cant figure out the break thing...

i praise you 110Leaded for figuring out this problem that everyone has had...
FTW!!!

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